Writing the Research Paper (100 points)

A single paper in the style of a journal article
submitted for publication is due after
the last day of laboratory class. Drafts of each stage
of the paper will be evaluated during the course and
must be turned in with the final paper.

Do not worry about "perfection" with your FIRST DRAFTS;
you need something to work with, and that is why it's called
a "draft."

The only way to have something to revise is to write something down in the first place.

The two main reasons I require you to write drafts of each section are
1) making you write something at intervals prevents your waiting
until the night before the final paper is due to start writing
2) turning in a draft lets me give you feedback on each section
and allows you time to revise your work for the final paper

Submit all work in its final form (i.e., NOT handwritten,
on a computer disk, as an attachment, or in an e-mail message)--ONLY
printed documents will be accepted except in special circumstances
that must be approved by me in advance of the due date.

For your own protection, I will make a copy of your final
paper to keep on file. When you submit your final paper,
please put your work loosely in a paper folder with pockets
(not the kind with 3-rings); do NOT use staples or paper
clips. Put your name and lab section on the OUTSIDE of the
folder.

A scientific research paper is traditionally divided into
four sections: introduction, materials and methods, results,
and discussion. These sections are typically completed through
an iterative process because no single section can be written
without consideration of another. The introduction is compiled
from reference material and reflects the thought processes
or lines of reason that lead you to perform experiments in
the laboratory. The remainder of the paper is constructed concurrently
as the experiment is constructed and planned. In the final
draft the organization of the materials and methods section
is coordinated with the results section. The results section
presents pertinent data in nearly chronological order and directs
the reader along the same mental paths through the data that
you took in solving the problem. The discussion section provides
interpretation of the data and projections as to the meaning
of the results. The use of good references throughout the paper
gives the work credibility by demonstrating an awareness of
previous works.

Writing a scientific article is not an easy task no matter how simple the actual experiment or concept. Practice, good planning, and organized record keeping are the only means to simplify the process. Revising your work, sometimes several times, is essential to producing a good final paper (see McMillan, pp. 126-160 (3rd ed.) or 167-205 (4th ed.)).

Special notes for the research paper for BIOC 311

Be aware of flaws or weaknesses in your data but do not belabor them with infinite analysis. Exceptions and inconsistency in your data should be mentioned and unsettled points described briefly.

If the data are substantially flawed you will not include
them in the paper; however, you should analyze and discuss
YOUR data in your lab notebook.

You can use data from anyone CURRENTLY taking BIOC 311 (i.e., any student, in any section, THIS SEMESTER ONLY!!) or any other
data that I upload into OWL-Space; acknowledge the SOURCE (i.e., include the names) of data in your final paper: "raw data" such as values for purification table, Km's, and gel images will be uploaded to the BIOC 311 Resources folder on OWL-Space; if you have especially nice results, e-mail them to me (Excel file for numbers, jpg's for images) and I'll upload them.

Remember that this writing assignment is to emulate a paper for publication, which is substantially different from a "laboratory report."

The abstract is a concise, complete report of a scientific investigation that "stands alone" without further explanation. The abstract is typically ONE paragraph with 200 to 250 words. Lengthy discussions and references to the literature are omitted from the summary/abstract.

The Introduction should "introduce" the paper. The reader should be presented with enough background information to be able to understand and evaluate the purpose of your study without having to refer to other works. The rationale for the study should be presented. Provide salient references but avoid trying to make an exhaustive review of the topic.

In the introduction, define the problem clearly. If the problem is not stated in a reasonable, understandable way, the reader will have no interest in your solution. Follow with some review of the literature to allow the reader to understand why the study is necessary and how you attempted to resolve it. Talk in general terms about techniques used to solve the problem, if necessary, but do not present any specifics about the protocols here. The final portion should be the statement of the principal results.

This section should be the easiest to write if you have good notebook skills. A well written Experimental Procedures section allows a competent scientist to duplicate your results. Present specific information about your materials. The suppliers and purity of reagents can be useful bits of information. Present methods in logical order but related methodologies can be grouped as a section. Be succinct when describing the protocols. Strive for the minimum of information that would allow another competent scientist to duplicate your results but be careful that essential information is included. The use of subheadings is recommended and should be coordinated with the results section. When a method is used that has been well described in another article, reference the specific article describing a method but outline the basic premise while stating the reference.

Ask yourself this question: Could someone else follow my words in this section and perform the same experiment with the same results?

Results (20 points)
*McMillan, pp. 66-71 (3rd ed.) or 83-89 (4th ed.)

Open the Results section by presenting the "big picture" or overview of the experiments. Focus on the theoretical question at hand and do not repeat the experimental details described in the Experimental Procedures. Orient and prepare the reader for the data that follows.

The data must direct the reader toward the solution to the problem. Organize the data in logical steps that describe the trail of investigation you followed in order to reach your conclusions. If your logic is sound, the reader will easily understand why you performed certain measurements and will be interested in the actual data obtained.

Data is presented in text, tables or graphs depending on the material and the emphasis that you desire.
Look at published examples of graph and table presentation and
mimic that style. Each figure or graph must be able to "stand
alone" with its figure legend. A descriptive title
includes why the figure is important (NOT merely "SDS Gel"). Present
information in the figure and legend as if this were all the
reader would see for this point. Discriminate
what data you present by using only the data relevant to the
conclusions drawn from the study. (The preceding statement
is made to keep the study focused NOT to intentionally disregard
conflicting data. Please maintain high ethical standards in
your scientific endeavors.) Present only representative
data not endless repetitions of the same data. Keep the presentations
concise and make the reading of your data as pleasant as possible.
Interest fades quickly if the reader has to work hard to figure
out what is being presented or why.

Choosing a method for clear presentation of your data depends on the type of information. (See McMillan, pp. 30-50 (3rd ed.) or 33-67 (4th ed.).)If one or only a few determinations or differences are presented it is best to use only text. Repetitive measurements may be presented in tables or graphs. Always consider describing the results in text and ifthe text version is too complex or cumbersome then a table or graph may be warranted. Avoid redundancy when stating summary of data in text that is presented in tabular form.

Be certain that any numbers that you present are statistically valid. Specifically, pay close attention to significant figures.

Clarity in the Results is paramount. This is the new information that you are presenting to the scientific community. All the other components of the paper are judged by the Results. The Introduction and the Materials and Methods section tell why and how you got the results and the Discussion tells what the results mean.

The Discussion is likely the most difficult section to write and define. Many papers submitted for publication are rejected based on problems with the Discussion. There is no ruler for how long a discussion should be. State your interpretation of the results clearly to lead the reader through your conclusions, then end the paper with a summary of the significance of the study.

Do NOT simply restate the Results.

Compare your results and conclusions with published materials. Clearly contrast and compare your interpretations with previous studies and findings.

Discuss the theoretical implications of your work and practical applications that you foresee. Be careful to keep your theoretical projections in proportion to the scope of your experiment. Leave most of the speculation to the readers.

Present the interpretation of your findings as clearly as possible. Present a summary of evidence for each major finding.

Make succinct concluding statements at the end of the discussion.
These conclusions may be what people remember most about your study.

NOTE: Your paper will be evaluated on two additional areas; for specific items, see the rubric for the final paper: